Variant report

Variant	rs7913442
Chromosome Location	chr10:95513408-95513409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr10:95513374-95513778	A549	lung:	n/a	n/a
2	FOXA1	chr10:95513384-95513675	T-47D	breast:	n/a	n/a
3	NR3C1	chr10:95513357-95513791	A549	lung:	n/a	n/a
4	TCF7L2	chr10:95513338-95513882	HEK293	kidney:	n/a	chr10:95513790-95513799 chr10:95513787-95513803 chr10:95513787-95513803 chr10:95513791-95513801 chr10:95513791-95513800 chr10:95513788-95513802

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:95499932..95502310-chr10:95511778..95514024,2	MCF-7	breast:
2	chr10:95510815..95514212-chr10:95521474..95524274,4	MCF-7	breast:

Variant related genes	Relation type
LGI1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10882327	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2095889	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2095890	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2095891	0.94[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758534	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069934	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069940	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7099740	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7894449	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs946553	0.82[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3346948	chr10:95421957-95532625	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7913442	CEP55	cis	parietal	SCAN
rs7913442	NUDT9P1	cis	parietal	SCAN
rs7913442	FRA10AC1	cis	parietal	SCAN
rs7913442	FRA10AC1	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95505800-95517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:95508200-95515000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:95509200-95514600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:95509600-95514800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:95509800-95514000	Weak transcription	Small Intestine	intestine
6	chr10:95510200-95517600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr10:95510800-95514400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:95511000-95516800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr10:95511000-95517600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:95511600-95513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:95511600-95517600	Enhancers	Fetal Stomach	stomach
12	chr10:95511800-95514200	Enhancers	Stomach Mucosa	stomach
13	chr10:95512000-95513800	Weak transcription	Colonic Mucosa	Colon
14	chr10:95512000-95515200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:95512000-95516000	Enhancers	Rectal Smooth Muscle	rectum
16	chr10:95512000-95516200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:95512000-95516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:95512000-95516600	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:95512000-95516800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr10:95512000-95516800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:95512000-95517000	Weak transcription	Fetal Brain Male	brain
22	chr10:95512000-95517200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:95512000-95517600	Weak transcription	Lung	lung
24	chr10:95512000-95517600	Weak transcription	Psoas Muscle	Psoas
25	chr10:95512000-95517800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr10:95512000-95522200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr10:95512200-95513600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:95512200-95514000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr10:95512200-95514600	Enhancers	Brain Anterior Caudate	brain
30	chr10:95512200-95516000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr10:95512200-95516600	Weak transcription	Brain Substantia Nigra	brain
32	chr10:95512200-95516600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr10:95512200-95517000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr10:95512200-95517600	Weak transcription	Liver	Liver
35	chr10:95512200-95517600	Enhancers	Colon Smooth Muscle	Colon
36	chr10:95512400-95516000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr10:95512600-95513600	Weak transcription	Right Atrium	heart
38	chr10:95512600-95513800	Weak transcription	Esophagus	oesophagus
39	chr10:95512600-95515400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:95512600-95515400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr10:95512600-95516800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr10:95512600-95517000	Weak transcription	Fetal Brain Female	brain
43	chr10:95512600-95522800	Weak transcription	Gastric	stomach
44	chr10:95512800-95513600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr10:95512800-95515600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr10:95512800-95516000	Weak transcription	Brain Angular Gyrus	brain
47	chr10:95512800-95517600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:95513000-95513800	Enhancers	Stomach Smooth Muscle	stomach
49	chr10:95513000-95514000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr10:95513000-95515000	Weak transcription	Osteobl	bone

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